You said that the doctors have done blood tests - do you know if they have specifically tested her for Lupus? Traditionally, the disease rears it's head in females during their 20's and 30's. The rashes normally associated with lupus appear after sun exposure. Has your mom been diagnosed with Rheumatoid Arthritis (in the same family as lupus) related to the swollen joints? Did the swollen joints' onset come after the virus?
You mentioned chronic fatigue as well - is that related to her virus or has she had it prior to the infection? What sort of doctors/specialists has she seen?
I know it's terrible having to watch her go through this, but you don't want your mom to have Lupus, as much as you want a diagnosis. It's not a condition that can be "fixed" with a pill.
Sorry about all the questions, but maybe we can point you in the right direction.